Get Started with ssdtools

Introduction

ssdtools is an R package to fit Species Sensitivity Distributions (SSDs) using Maximum Likelihood and model averaging.

SSDs are cumulative probability distributions that are used to estimate the percent of species that are affected by a given concentration of a chemical. The concentration that affects 5% of the species is referred to as the 5% Hazard Concentration (\(HC_5\)). For more information on SSDs the reader is referred to Posthuma, Suter II, and Traas (2001).

In order to use ssdtools you need to install R (see below) or use the Shiny app. The shiny app includes a user guide. This vignette is a user manual for the R package.

Philosophy

ssdtools provides the key functionality required to fit SSDs using Maximum Likelihood and model averaging in R. It is intended to be used in conjunction with tidyverse packages such as readr to input data, tidyr and dplyr to group and manipulate data and ggplot2 (Wickham 2016) to plot data. As such it endeavors to fulfill the tidyverse manifesto.

Installing

In order to install R (R Core Team 2018) the appropriate binary for the users operating system should be downloaded from CRAN and then installed.

Once R is installed, the ssdtools package can be installed (together with the tidyverse) by executing the following code at the R console

install.packages(c("ssdtools", "tidyverse"))

The ssdtools package (and ggplot2 package) can then be loaded into the current session using

library(ssdtools)
library(ggplot2)

Getting Help

To get additional information on a particular function just type ? followed by the name of the function at the R console. For example ?ssd_gof brings up the R documentation for the ssdtools goodness of fit function.

For more information on using R the reader is referred to R for Data Science (Wickham and Grolemund 2016).

If you discover a bug in ssdtools please file an issue with a reprex (repeatable example) at https://github.com/bcgov/ssdtools/issues.

Inputting Data

Once the ssdtools package has been loaded the next task is to input some data. An easy way to do this is to save the concentration data for a single chemical as a column called Conc in a comma separated file (.csv). Each row should be the sensitivity concentration for a separate species. If species and/or group information is available then this can be saved as Species and Group columns. The .csv file can then be read into R using the following

data <- read_csv(file = "path/to/file.csv")

For the purposes of this manual we use the CCME dataset for boron.

ccme_boron <- ssddata::ccme_boron
print(ccme_boron)
#> # A tibble: 28 × 5
#>    Chemical Species                  Conc Group        Units
#>    <chr>    <chr>                   <dbl> <fct>        <chr>
#>  1 Boron    Oncorhynchus mykiss       2.1 Fish         mg/L 
#>  2 Boron    Ictalurus punctatus       2.4 Fish         mg/L 
#>  3 Boron    Micropterus salmoides     4.1 Fish         mg/L 
#>  4 Boron    Brachydanio rerio        10   Fish         mg/L 
#>  5 Boron    Carassius auratus        15.6 Fish         mg/L 
#>  6 Boron    Pimephales promelas      18.3 Fish         mg/L 
#>  7 Boron    Daphnia magna             6   Invertebrate mg/L 
#>  8 Boron    Opercularia bimarginata  10   Invertebrate mg/L 
#>  9 Boron    Ceriodaphnia dubia       13.4 Invertebrate mg/L 
#> 10 Boron    Entosiphon sulcatum      15   Invertebrate mg/L 
#> # ℹ 18 more rows

Fitting Distributions

The function ssd_fit_dists() inputs a data frame and fits one or more distributions. The user can specify a subset of the following 10 distributions

ssd_dists_all()
#>  [1] "burrIII3"      "gamma"         "gompertz"      "invpareto"    
#>  [5] "lgumbel"       "llogis"        "llogis_llogis" "lnorm"        
#>  [9] "lnorm_lnorm"   "weibull"

using the dists argument.

fits <- ssd_fit_dists(ccme_boron, dists = c("llogis", "lnorm", "gamma"))

Coefficients

The estimates for the various terms can be extracted using the tidyverse generic tidy function (or the base R generic coef function).

tidy(fits)
#> # A tibble: 6 × 4
#>   dist   term           est    se
#>   <chr>  <chr>        <dbl> <dbl>
#> 1 llogis locationlog  2.63  0.248
#> 2 llogis scalelog     0.740 0.114
#> 3 lnorm  meanlog      2.56  0.235
#> 4 lnorm  sdlog        1.24  0.166
#> 5 gamma  scale       25.1   7.64 
#> 6 gamma  shape        0.950 0.223

Plots

It is generally more informative to plot the fits using the autoplot generic function (a wrapper on ssd_plot_cdf()). As autoplot returns a ggplot object it can be modified prior to plotting.

theme_set(theme_bw()) # set plot theme

autoplot(fits) + 
  ggtitle("Species Sensitivity Distributions for Boron") +
  scale_colour_ssd()

Selecting One Distribution

Given multiple distributions the user is faced with choosing the “best” distribution (or as discussed below averaging the results weighted by the fit).

ssd_gof(fits)
#> # A tibble: 3 × 9
#>   dist      ad     ks    cvm   aic  aicc   bic delta weight
#>   <chr>  <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>
#> 1 llogis 0.487 0.0994 0.0595  241.  241.  244.  3.38  0.11 
#> 2 lnorm  0.507 0.107  0.0703  239.  240.  242.  1.40  0.296
#> 3 gamma  0.440 0.117  0.0554  238.  238.  240.  0     0.595

The ssd_gof() function returns three test statistics that can be used to evaluate the fit of the various distributions to the data.

• Anderson-Darling (ad) statistic,
• Kolmogorov-Smirnov (ks) statistic and
• Cramer-von Mises (cvm) statistic

and three information criteria

• Akaike’s Information Criterion (aic),
• Akaike’s Information Criterion corrected for sample size (aicc) and
• Bayesian Information Criterion (bic)

Note if ssd_gof() is called with pvalue = TRUE then the p-values rather than the statistics are returned for the ad, ks and cvm tests.

Following Burnham and Anderson (2002) we recommend the aicc for model selection. The best predictive model is that with the lowest aicc (indicated by the model with a delta value of 0.000 in the goodness of fit table). In the current example the best predictive model is the gamma distribution but the lnorm distribution has some support.

For further information on the advantages of an information theoretic approach in the context of selecting SSDs the reader is referred to Fox et al. (2021).

Averaging Multiple Distributions

Often other distributions will fit the data almost as well as the best distribution as evidenced by delta values < 2 (Burnham and Anderson 2002). In this situation the recommended approach is to estimate the average fit based on the relative weights of the distributions (Burnham and Anderson 2002). The aicc based weights are indicated by the weight column in the goodness of fit table. In the current example, the gamma and log-normal distributions have delta values < 2.

Estimating the Fit

The predict function can be used to generate model-averaged (or if average = FALSE individual) estimates by parametric bootstrapping. Model averaging is based on aicc unless the data censored is which case aicc in undefined. In this situation model averaging is only possible if the distributions have the same number of parameters. Parametric bootstrapping is computationally intensive. To bootstrap for each distribution in parallel register the future backend and then select the evaluation strategy.

doFuture::registerDoFuture()
future::plan(future::multisession)

set.seed(99)
boron_pred <- predict(fits, ci = TRUE)

The resultant object is a data frame of the estimated concentration (est) with standard error (se) and lower (lcl) and upper (ucl) 95% confidence limits (CLs) by percent of species affected (percent). The object includes the number of bootstraps (nboot) data sets generated as well as the proportion of the data sets that successfully fitted (pboot). There is no requirement for the bootstrap samples to converge.

boron_pred
#> # A tibble: 99 × 8
#>    dist    percent   est    se   lcl   ucl nboot pboot
#>    <chr>     <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1 average       1 0.379 0.391 0.122  1.58  1000     1
#>  2 average       2 0.624 0.540 0.213  2.25  1000     1
#>  3 average       3 0.856 0.656 0.305  2.78  1000     1
#>  4 average       4 1.08  0.756 0.405  3.27  1000     1
#>  5 average       5 1.31  0.845 0.509  3.74  1000     1
#>  6 average       6 1.53  0.926 0.617  4.17  1000     1
#>  7 average       7 1.76  1.00  0.730  4.55  1000     1
#>  8 average       8 1.98  1.07  0.852  4.92  1000     1
#>  9 average       9 2.21  1.14  0.972  5.30  1000     1
#> 10 average      10 2.44  1.20  1.09   5.66  1000     1
#> # ℹ 89 more rows

The data frame of the estimates can then be plotted together with the original data using the ssd_plot() function to summarize an analysis. Once again the returned object is a ggplot object which can be customized prior to plotting.

ssd_plot(ccme_boron, boron_pred,
         color = "Group", label = "Species",
         xlab = "Concentration (mg/L)", ribbon = TRUE) + 
  expand_limits(x = 5000) + # to ensure the species labels fit
  ggtitle("Species Sensitivity for Boron") +
  scale_colour_ssd()

In the above plot the model-averaged 95% confidence interval is indicated by the shaded band and the model-averaged 5% Hazard Concentration (\(HC_5\)) by the dotted line. Hazard concentrations are discussed below.

Hazard Concentrations

The 5% hazard concentration (\(HC_5\)) is the concentration that affects 5% of the species tested.

set.seed(99)
boron_hc5 <- ssd_hc(fits, ci = TRUE)
print(boron_hc5)
#> # A tibble: 1 × 10
#>   dist    percent   est    se   lcl   ucl    wt method     nboot pboot
#>   <chr>     <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>      <dbl> <dbl>
#> 1 average       5  1.31 0.797 0.505  3.53     1 parametric  1000     1

Plotting

The ssdtools package provides four ggplot geoms to allow you construct your own plots.

The first is geom_ssdpoint() which plots species sensitivity data

ggplot(ccme_boron) +
  geom_ssdpoint(aes(x = Conc))

The second is geom_ssdsegments() which plots the range of censored species sensitivity data

ggplot(ccme_boron) +
  geom_ssdsegment(aes(x = Conc, xend = Conc * 2))

The third is geom_xribbon() which plots species sensitivity confidence intervals

ggplot(boron_pred) +
  geom_xribbon(aes(xmin = lcl, xmax = ucl, y = percent/100))

And the fourth is geom_hcintersect() which plots hazard concentrations

ggplot() +
  geom_hcintersect(xintercept = c(1, 2, 3), yintercept = c(5, 10, 20) / 100)

They can be combined together as follows

gp <- ggplot(boron_pred, aes(x = est)) +
  geom_xribbon(aes(xmin = lcl, xmax = ucl, y = percent/100), alpha = 0.2) +
  geom_line(aes(y = percent/100)) +
  geom_ssdsegment(data = ccme_boron, aes(x = Conc / 2, xend = Conc * 2)) +
  geom_ssdpoint(data = ccme_boron, aes(x = Conc / 2)) +
  geom_ssdpoint(data = ccme_boron, aes(x = Conc * 2)) +
  scale_y_continuous("Species Affected (%)", labels = scales::percent) +
  expand_limits(y = c(0, 1)) +
  xlab("Concentration (mg/L)")
print(gp + geom_hcintersect(xintercept = boron_hc5$est, yintercept = 5 / 100))

To log the x-axis add the following code.

gp <- gp + coord_trans(x = "log10") +
  scale_x_continuous(
    breaks = scales::trans_breaks("log10", function(x) 10^x),
    labels = comma_signif
  )
print(gp + geom_hcintersect(xintercept = boron_hc5$est, yintercept = 5 / 100))

The most recent plot can be saved as a file using ggsave(), which also allows the user to set the resolution.

ggsave("file_name.png", dpi = 600)